Hi Paul,

Thank you for replying me! Another question: How do I know the total number of voxels in an image? 

Mingxia

On Tue, Jul 7, 2015 at 4:35 PM, paul mccarthy <[log in to unmask]> wrote:

Hi Zhang,

You can do this using fslstats - first, calculate the proportion of 100 voxels relative to the total size of your image:

  prop = 100 / <total number of voxels in your image>

Then use fslstats to find the percentile value at this proportion:

  fslstats <my_image> -p <100 - 100 * prop>

(Use '-a' before '-p' if you are interested in absolute values)

You can then use this percentile value as a threshold in fslmaths, to create a mask containing the 100 voxels with the highest intensity:

  fslmaths <my_image> -thr <threshold_from_fslstats> -bin <my_mask>

Cheers,

Paul

On 7 July 2015 at 07:01, zhang mingxia <[log in to unmask]> wrote:

Hi Iwo,

I don't want to creat a sphere ROI. I want the 100 voxels with the largest z value in zstat.nii.gz to be the ROI mask. My question is how to find out the 100 voxels with largest z value in zstat.nii.gz?

Thank you again!

Mingxia Zhang 

On Mon, Jul 6, 2015 at 7:28 PM, Iwo Bohr <[log in to unmask]> wrote:

Sorry, one correction to the previous message: the coordinates of the ROI central point are expressed in voxels, not in mm! (see below)

Iwo

----- Forwarded Message -----
From: Iwo Bohr <[log in to unmask]>
To: [log in to unmask]
Sent: Monday, 6 July 2015, 12:22
Subject: Re: [FSL] making mask of a fixed number of voxels of the most responsive ones

In terms of creating your ROI these two commands could be helpful:

1) fslmaths /usr/local/fsl/data/standard/MNI152_T1_2mm -mul 0 -add 1 -roi $c1 1 $c2 1 $c3 1 0 1 ${out}point -odt float
2) fslmaths ${out}point -kernel sphere $rad -fmean ${out}$name -odt float

where:

$c1-$c3 are x,y,z coordinates (voxels) of the centre

$rad : to replaced by the radius (mm)

The above is for creating a  ROI in the MNI space, but it could be replaced by any space.

First command creates the centre of the ROI, second the spherical ROI (centred around the point).

Hope this helps,

Iwo

---

From: zhang mingxia <[log in to unmask]>
To: [log in to unmask]
Sent: Monday, 6 July 2015, 10:39
Subject: [FSL] making mask of a fixed number of voxels of the most responsive ones

Dear FSL experts,

I need to create a mask of the most responsive voxels. Specifically, in my study , I got the z value image of one condition (e.g., zstat1.nii.gz). Now, I need to create a mask of a fixed number of voxels(e.g., 100) with max z value in zstat1.nii.gz. Does any one know how I can do?

Thanks in advance!

Mingxia Zhang